Laurence Slavin, a partner at specialist medical accountants Ramsay Brown and Partners, said it was 'common' for GPs to query their payments from PCTs each month.
But he warned that as PCTs slash staff in preparation for mergers they would be unable to deal with queries from GP practices that believed they had been underpaid. Some London PCTs he dealt with were planning to cut hundreds of staff, Mr Slavin said.
Meanwhile, the National Association of Primary Care (NAPC) urged GP consortia to talk to PCTs about clustering to prevent problems.
Mr Slavin said GPs may have to wait months for underpayments to be remedied, leaving some with cashflow problems.
'GPs are concerned that the pace of change is such that there won't be individuals in the PCTs able to deal with their queries,' he said.
'If they have queries about their income or they haven't been paid for something then there won't be anyone at the PCT to sort it out.'
GPC negotiator Dr Beth McCarron-Nash said she was aware that some PCTs were finding it 'exceptionally difficult', but added the situation was variable.
She said: 'Some PCTs have been described as imploding, but in other areas PCTs are continuing to function well.'
But Dr McCarron-Nash said it 'makes sense' for PCTs to cluster in order to manage their functions.
Meanwhile, the NAPC has urged GP consortia to take an 'active interest' in the establishment of PCT clusters.
NAPC chairman Dr Johnny Marshall said GP involvement in plans to merge PCTs was vital to ensure that they will be able to continue to provide support to GP consortia.
Dr Charles Alessi, a GP in Surrey and a member of NAPC's executive, said the association was talking with SHAs to ensure GPs have a say in the role and functions of PCT clusters.